3D Gene Expression

Expression Atlases
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Data Releases

   Project Goals

   Staining & Mounting
   Probe Constructs


File Formats:
   PointCloud (.pce)
   VirtualEmbryo (.vpc)
   Correspondence files

The BDTNP is providing software developed to process, visualize and analyze 3D gene expression data.
  • PointCloudXplore: Visualization and analysis of the data in PointCloud and Virtual Embryo Files.
  • PointCloudToolBox: Image analysis methods to generate PointCloud files that contain geometric data for each nucleus (position, volume, etc.), and the measured levels of gene expression in a single embryo.
  • PointCloudAlign: Registration methods to place gene expression data from many embryos into a VirtualEmbryo file, to allow comparison between the expression patterns of more than two or three genes.
  • Nonparametric Identification of Regulatory Interactions (NODE): A method that determines the correlation between transcription factor protein concentrations and temporal changes in the mRNA expression of putative target genes for small clusters of cells throughout the embryo.
  • Biological Imaging Database (BID): A relational database, and web-based user interface, for tracking 3D gene expression experiments. The source code and instructions are available upon request.